Sequencing ocean's dna reveals a hidden world

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(NC&T/UCD) Most of the microbes on the planet -- and therefore most, by far, of all the living things on Earth -- cannot be grown in a laboratory, said Jonathan Eisen, an author on two of the research papers and of one review paper published in the journal PLoS Biology. Eisen is a professor at the UC Davis Genome Center, the Department of Medical Microbiology and Immunology, and the Section of Evolution and Ecology.

In his review article, Eisen describes "environmental shotgun sequencing," one of the main methods used in the study. Instead of trying to sequence the genome of a single animal, plant or microbe in isolation, environmental shotgun sequencing scoops up all the DNA in one go, sequences it and produces a "metagenome" that includes the genomes of all the organisms present.

"This is the only way you can study these natural microbial communities," he said. It gives a view of the entire community, not just individuals.

Between August 2003 and May 2004, the yacht Sorcerer II sailed from northeastern Canada to the South Pacific, via the Caribbean, the Panama Canal and the Galapagos Islands. The crew collected water samples from different marine environments and filtered them to extract microbes.

Then came the hard part. The researchers sequenced the microbe DNA in short chunks, then assembled the 6.5 million "reads" into a map that included the genomes of all the microbes captured in the water. Eisen compared the process to reconstructing an entire library from the scraps of pages torn from thousands of different books.

The study provides new insights into the extraordinary size and diversity of the microscopic life in the ocean. For example, the results almost double the number of proteins known to science. They also give insights into how microorganisms adapt to different conditions, for example light and salinity, in different parts of the ocean.

The Sorcerer II expedition was funded by the U.S. Department of Energy, the Gordon and Betty Moore Foundation, the Discovery Channel and the J. Craig Venter Foundation.